On one of his operations, he initiated a black mark by going on an unsanctioned rescue mission to save the lives of three servicemen. Another unsanctioned op was to save the life of his friend, CaptainLyle Holland, whose Apache helicopter had crashed in Afghanistan. The mission, however, was unsuccessful. He was later forced to relive this memory when his team went to find out what happened to MajorLeonard's team on M1B-129. (ATL: "Rising", "The Intruder", "Phantoms")

with a Wraith spear gun by a Wraith Commander and brought before the Wraith Keeper. He was questioned by the Keeper about how he acquired the Life signs detector but Ford, who followed Sheppard's boot trail, arrived saved him from being feed on. They then blew the C-4 and escaped back to the Puddle Jumper but with the unfortunate result of awakening the Wraith from their hibernation cycle fifty years prematurely. On the way back to the Spacegate, three Darts were blocking the way. He used drones to destroy one of them and lure the others away from the gate so Ford could dial and send his IDC before returning to Atlantis. With the loss of Colonel Sumner, Sheppard was left to command the military contingent of Atlantis. He also took up the command of the First Atlantis Reconnaissance Team with Ford, Teyla, and Dr.Rodney McKay, spearheading the expedition's efforts to explore the Pegasusgalaxy. (ATL: "Rising")

Wraith feeding. He offered Dr.Carson Beckett's assistance in perfecting the drug. When Beckett reached the point where the drug required human testing, he convinced Dr.Elizabeth Weir to allow them to test it on Steve. After the test of the drug killed Steve, he warned Druhin that the Wraith would exterminate them when a single Wraith dies from the drug. Druhin refused and began administering it to the population. When half the people that received the drug fell ill and died, he took his team back to Atlantis. (ATL: "Poisoning the Well")

When the Atlantis expedition was running low on food, Teyla Emmagan brought he and his team to the Genii homeworld and introduced them to Tyrus and his daughter Sora Tyrus. After meeting with Cowen and coming to an agreement on trading C-4 and medical supplies for food, Teyla and Lt.Aiden Ford stayed for the harvest ceremony while he and Dr.Rodney McKay returned to Atlantis to discuss the trade deal with Dr.Elizabeth Weir. When he and McKay returned and found a secret Underground Bunker, they were arrested and Teyla and Ford were brought inside. Cowen revealed that the Genii Confederation used to span many worlds but was forced to hide in the bunker and pose as simple farmers to fool the Wraith. When Cowen revealed their plan to use the C-4 to complete their nuclear weapons, he offered McKay's help in speeding up their completion. After a loose alliance was formed between the two, he and his team joined Cowen and Tyrus on a mission to a WraithHive ship. Once on the Hive, he, McKay and Cowen infiltrated a room with a data core and they download information to the Wraith data storage device. They returned to the Puddle Jumper and returned to the Genii homeworld. When they landed, Cowen tried to double-cross them and he drew his weapon but was not forced to fire as Cowen surrendered when two Jumpers decloaked. Upon returning to Atlantis, Dr.Peter Grodin analyzed the data on the device and discovered there were at least 60 Hive ships in the Pegasusgalaxy. (ATL: "Underground")

After the discovery of M5S-224's powerful atmosphere, he traveled to Earth with Teyla Emmagan to brief Stargate Command on the situation in the Pegasusgalaxy. After the briefing, Sheppard took Teyla shopping and began to notice something was wrong. He instructed the driver assigned to him to take them to the apartment of his dreams. After they arrived and some of his deceased friends began to arrive, he knew something was wrong and shot one of them to see if they were real. Fortunately, this was all an illusion created by the inhabitants of the planet and he never left Pegasus. (ATL: "Home")

During a trip to the mainland with Teyla Emmagan, they discovered a storm approaching Atlantis. He and Lt.Aiden Ford traveled to Manara to negotiate with Smeadon about evacuating the Atlantis expedition there. After Dr.Rodney McKay and Dr.Radek Zelenka came up with a plan to use lightning to power Atlantis' shield and nonessential personnel were evacuated, he uncoupled one of the four Grounding stations and headed for the fourth when a Genii strike force under Acastus Kolya gated to Atlantis. After McKay was able to activate the radio and inform him that the Genii were after the C-4, he was able to get to the armory first and hide it. After McKay was tortured into revealing his plan to save the city, Kolya contacted him and demanded he uncouple the last grounding station or he would kill Dr.Elizabeth Weir. When he reached the grounding station, he was ambushed by two Genii soldier but was able to kill them with help from his Life signs detector. After contacting Kolya and informing him of the failure of his men, Kolya lied and said he killed Weir. After avoiding an ambush from three Genii soldiers, he disabled the Naquadah generator that powers Stargate Operations and infiltrated it. After knocking Ladon Radim unconscious, he activated the Stargate shield killing fifty-five Genii soldiers when they attempted to send reinforcements through the Stargate. After retreating from Stargate Operations, he was contacted by Kolya and he demanded he reactivate the generators or he would kill McKay and Weir. While reactivating one of the generators, he was captured by two Genii soldiers but was saved by Teyla, Ford and Dr.Carson Beckett who returned from the mainland. They planed to attack Stargate Operations together and he sent Teyla and Beckett to fly a Puddle Jumper into the room to create a distraction while he and Ford went in on foot. The Genii eventually decided to retreat, trying to take Weir and McKay with them so he was forced to attack before the Jumper was in the room. McKay got away and Sheppard was able to save Weir by hitting Kolya in the shoulder. McKay is then able to raise the shield and save the city from the tidal wave. (ATL: "The Eye", "The Storm")

When Dr.Brendan Gall located the last remaining Lagrangian Point satellite, he along with a team of Gall, Dr.Rodney McKay and Dr.Abrams went on a mission in a Puddle Jumper to investigate. When they arrived, they detected a distress call from a nearby planet. Once they got clearance from Dr.Elizabeth Weir, they landed on the planet and headed for the Wraith supply ship. Once inside the ship, they discovered several Wraith warriors that had been fed upon. After splitting up to search the ship, McKay realized that the cocoons could keep Humans alive indefinitely if they had a large enough power source and there could still be survivors. He radioed Gall and Abrams and ordered them to fall back to the Jumper. On the way back, Gall and Abrams are attacked by a Wraith survivor. It fed on Abrams and took Gall. He and McKay came on Abrams' body and took his weapons and found two Wraith grenades on a dead Wraith warrior. After hearing Gall scream, they were able to locate him but he had been fed upon but was still alive. He ordered McKay to stay with Gall while he went after the Wraith that was heading for the Jumper. When he caught up to the Wraith, it had already made it to the Jumper. After luring the Wraith into the open, he shot him several times with his FN P90 Personal Defense Weapon but the Wraith healed itself and grabbed a M9 pistol from the Jumper and shot him in the arm and disabled his P90. After bandaging his arm, he used a flare to lure the Wraith out of the Jumper and tried to enter it but the Wraith protected it with a shield. He then used one of the grenades as a mine but the Wraith survived and he fired on him with his sidearm until he was out of ammo. The Wraith was about to feed on him when McKay arrived and fired on him with his sidearm. When Lt.Aiden Ford and Teyla Emmagan arrived in orbit above the planet in a Jumper, he used a energy bar to attract the Light bugs to the Wraith and ordered them to fire a Drone weapon at the largest life signs reading killing the Wraith. (ATL: "The Defiant One")

On a mission to Proculus, his team'sPuddle Jumper was attacked by Wraith Darts. They were saved by a mysterious force from the planet below. After landing on the surface, they were introduced to Chaya Sar. In order to negotiate on allowing refugees to come to Proculus to be protected from the Wraith, he brought Chaya back to Atlantis and gave her a tour before taking her to see Dr.Elizabeth Weir. Weir offered Chaya's people technology in exchange for allowing the Athosians and Atlantis expedition members to evacuate there when the Wraith come. Chaya wished to see information on the various religions on Earth before making a decision and he took her on picnic where they kissed. During the next meeting, Dr.Rodney McKay, who was suspicious of Chaya's actions, scanned her and discovered she was an ascendedAncient. Before she could explain, Wraith attacked Proculus and she returned through the Stargate. He followed her and after she used her powers to defeat the Wraith, he went to the surface and explained that she used her powers to destroy a Wraith fleet long ago and was punished by the Others and forced to protect Proculus for the rest of time. Before he left, she shared herself with him. (ATL: "Sanctuary")

With three WraithHive ships on their way to Atlantis, he and Teyla Emmagan traveled to a planet in their path to do recon. They met with Orin a friend of Teyla's father and warned them of the approaching Wraith and told him and his family to meet them in the forest after dark. They headed into orbit and scanned the fleet as it exited hyperspace. They headed back to the Stargate as Sheppard felt there wasn't enough time to save anyone but were cut off when the Wraith dialed in. They headed to the spot she told Orin and waited for him. After seeing the Wraith hit the planet with a beam, he went to investigate on foot and when he returned Orin and his family as well as Arja and his family arrived and they headed back to Atlantis. After they arrived Dr.Elizabeth Weir asked him to record a video message for ColonelMarshall Sumner's family to be sent with the transmission to Earth. (ATL: "Letters from Pegasus")

When Teyla Emmagan was having trouble sleeping, he asked Dr.Kate Heightmeyer to speak with her but she did not like his involvement in her life. After Charin gave Teyla the gate address of a planet where her ancestors were from, he and his team traveled to the planet and discovered a Wraith Lab that belonged to the Wraith Scientist that experimented on Teyla's ancestors. They discovered a Wraith data storage device and brought it back to Atlantis. Dr.Elizabeth Weir was able to translate the Wraith language and discovered that the Scientist was splicing Wraith DNA into Humans and Teyla has a small amount of Wraith DNA in her genetic makeup. Teyla then tried to tap into the Wraith telepathic network and connected with a Wraith on the approaching Hive ship. When the Wraith began to feed on someone, Weir ordered Dr.Carson Beckett to pull her out. She insisted on going back in and was taken over by the Wraith and Beckett pulled her out. While under Wraith control, she gave the position of the Alpha Site and it was attacked. She wanted to go back again because she was close to finding out the Wraith battle plan. Weir agreed and she was taken over again and had to be stunned by Sgt.Bates. When she awoke, she told them that the Wraith were coming to Atlantis to get to Earth. (ATL: "The Gift")

With three WraithHive ships heading to Atlantis, he was tasked by Dr.Elizabeth Weir in choosing a new Alpha Site. On a mission to M1M-316 he and his team encountered a Dinosaur like creature and had to evacuate. When they returned, Sgt.Bates accused Teyla Emmagan of disclosing information to the Wraith until he explained that it was not the Wraith that forced them to evacuate. Teyla followed Bates in the hall and confronted him. When Bates said he felt Teyla should not be allow to roam the city unescorted, she slugged him and he and Lt.Aiden Ford had to separate them. Later when Bates was attacked, Teyla was questioned by him but denied her involvement. This was proven true when Dr.Carson Beckett found Wraith DNA on Bates' uniform. After the location of the Wraith was discovered, he led the first team to search for him. After his team was stunned by the Wraith, Teyla and Ford's team double timed it to his position and stunned the Wraith before it could feed on Sheppard. Once the Wraith was in the Atlantis brig, Teyla tried to enter his mind to find out what he had done to the city but the Wraith attacked her mind and caused her great pain. Sheppard was forced to shoot the Wraith to stop him. After Dr.Rodney McKay was only able to destroy one of the Hives with the Lagrangian Point satellite, Weir ordered an evacuation. As they were leaving, they received an incoming wormhole from Earth. A team of Marines led by ColonelDillon Everett came through the Stargate. He informed Weir that he was taking command and his mission was to defend Atlantis until the Daedalus powered by a Zero Point Module arrives in four days. When Everett ordered Sheppard to contact the Alpha Site and recall all military personnel, Weir asked him to wait until she was briefed on the plan. After the briefing, he trained the new pilots on the Puddle Jumpers and deployed Nuclear warheads in orbit. During the first wave of Wraith Darts, he manned the AncientControl chair and used Drone weapons to fight off the Darts. Unfortunately, this depleted the drones and he had the idea of remote controlling the Jumpers and using Genii A-bombs to attack the Hives. While Weir traveled to the Genii homeworld and McKay worked on remote controlling the Jumpers, he and Ford helped sweep the city for Wraith intruders. After the Wraith took out one of the Naquadah generators, they headed for the closest one to help Teyla's team defend it and were able to defeat the remaining Wraith. After the Wraith launched a second wave, he went to the chair but the Mark II Naquadah generators powering the chair were depleted and remote controlling the Jumper was impossible. He chose to take one of the Jumpers on a suicide mission to destroy one of the Hives in orbit. The mission was successful, and Sheppard was saved by the timely arrival of the Daedalus who beamed him out. With one Hive still intact, he convinced ColonelSteven Caldwell to use the Asgard beaming technology to beam a nuke into the Hive. After the last Hive was destroyed and the remaining Darts impacted Atlantis' shield causing a radio black out, he feared the city had been destroyed and was relieved to hear Weir's voice. He was then beamed down to the city with several Marines to help with the Wraith in the city. After McKay discovered 12 more Hives on their way to Atlantis with the Long range sensors, he had the idea of setting up an ambush with the Daedalus at the Hives hyperspace pause location. When Weir approved the mission, he joined the Daedalus. After the ships exited hyperspace, the Daedalus was able to destroy two Hives before the Wraith used a Jamming code to block the beaming technology. After taking heavy damage, Caldwell retreated and entered hyperspace. Once back in Atlantis, the Wraith began to bombard the shield from orbit. He then came up with an idea to fake a self-destruct and then cloak the city. After Ford escaped from the infirmary, he went to search for him but was unable to stop him from getting to a Jumper and leaving through the Stargate. Fortunately, the Wraith fell for the ruse and left the system. (ATL: "The Siege, Part 1", "The Siege, Part 2", "The Siege, Part 3")

Not long after the thwarted invasion, Sheppard returned to Earth with several other senior members of the Expedition. At this point, The Pentagon's intention was to replace Sheppard with another, higher-ranking officer with a less spotted record, with Major GeneralHenry Landry indicating that ColonelSteven Caldwell was the preferred candidate. At the insistence of Dr.Elizabeth Weir, however, Sheppard was instead promoted to Lt. Colonel and appointed the expedition's permanent military commander. While on Earth, he visited Lt.Aiden Ford's cousin Lara and assured her that he would do everything in his power to find him. On the trip back to Atlantis on the Daedalus, Dr.Monroe was found dead. When Dr.Rodney McKay discovered that a Wraith computer virus was responsible, he worked with McKay and Hermiod to eradicate the virus. When the virus began broadcasting a distress call, he used an F-302 fighter-interceptor to destroy the communications array. After he destroyed it the virus took control of his 302 and he had to be beamed back to the ship. After a system shutdown was ineffective, he and McKay unplugged the navigational computers from the 302s and tried another shutdown but the virus returned. He realized the 302 he was beamed out of was following them and took a 302 to destroy it. He chased the virus controlled 302 near the corona of a Star and was able to destroy it. They preformed one last shutdown and eradicated the virus. When they returned to Atlantis, Teyla Emmagan gave him a report on the whereabouts of Ford. (ATL: "The Intruder")

When MajorEvan Lorne and Dr.Parrish were exploring P3M-736, they came across a Wraith corpse. Lorne sent the body back to Atlantis and Dr.Carson Beckett discovered the enzyme sack had been removed. He recognized that Lt.Aiden Ford was responsible and took his team and Lorne's team to the planet to search for him. During the search, he was paired up with Teyla Emmagan and they came across Ronon Dex who stunned them with his Particle magnum. They awoke tied up in a cave. Ronon explained that he was a Runner and that the Wraith were hunting him. Sheppard was able to convince him that they were not enemies and that Beckett could remove the Wraith tracker. Ronon allowed Sheppard to return to Atlantis and bring Beckett but kept Teyla as a hostage. After returning to the planet, he took up a sniper position while Beckett removed the tracker. After hearing Dr.Rodney McKay's gunfire, he headed to his location and confronted Ford. He was unable to convince him to go willingly and shot him in the leg. Ford then ran into the beam of one of the Wraith Darts that had just come through the Stargate. After returning to Atlantis, he sent a MALP to Ronon's homeworld of Sateda but the whole planet was destroyed. (ATL: "Runner")

He was on a mission on Thenora to search for any survivors during the Wraithculling there. However, there was none. On the way back to the Stargate, Dr.Rodney McKay and Lt.Laura Cadman were scooped up by a Wraith beam. He was able to shoot down the Wraith Dart. He brought Dr.Radek Zelenka be contacted to remove McKay and Cadman but there was only enough power to get one out. He randomly picked one and it turned out being McKay but unfortunately Cadman's mind was transferred into McKay. He ordered the remains of the Dart to be brought back to Atlantis. Back on Atlantis, he trained Ronon Dex in Tau'ri weapons and fighting techniques and was impressed with his skills. He convinced Ronon to stay on Atlantis and convinced Dr.Elizabeth Weir to allow him to join his team. (ATL: "Duet")

During Ronon Dex's first mission as part of his team, the team landed their Puddle Jumper on the penal island on the planet Olesia. When the prisoners attacked, Ronon was shot in the ankle with an arrow and he ordered a retreat. Fortunately, the Poros came and drove the prisoners back allowing the team to retreat to the Jumper. They were then lead to the city and greeted by the Magistrate. On their way back to the Stargate, their Jumper was shot down by the prisoners. They are captured and restrained by the leader Torrell. Eldon, the prisoner who designed the explosives and was assigned by Torrell to help Dr.Rodney McKay fix the Jumper, offered to free them if they take him with them. On the way to the Jumper, a Wraith Dart came through the gate. This forced the prisoners to abandon the Jumper and go into hiding. The team is then able to retake the Jumper and McKay works on the Dial Home Device. Unfortunately, the prisoners returned and attacked. He, Teyla and Ronon attempted to fight them off but were overrun. Torrell tries to force them to take the prisoners with them at gunpoint but Sheppard refuses. Suddenly, a Wraith cruiser approaches and McKay attempts to dial the gate but the power has cut out. Sheppard has him divert power to the Drone weapons and fires at the cruiser. Dr.Elizabeth Weir radios from a cloaked Jumper that the cruiser is damaged but two more are closing in. Sheppard tells her to dial one of the backup planets to the Alpha Site and the prisoners escape. She then dials Atlantis and the team along with Eldon escape the planet. (ATL: "Condemned")

On a mission to Doranda, the team discovers an Ancientoutpost. While Teyla Emmagan and Ronon Dex embarked on a trading mission to Belkan, he and Dr.Rodney McKay worked on the outpost to perfect Project Arcturus. After several failed simulations, McKay believed he had perfected the containment field and they prepared for a test. During the test, the field began to fail and McKay sent Dr.Collins to adjust the field manually. The field partially collapsed and Collins was killed form radiation poisoning. After returning to Atlantis, Dr.Elizabeth Weir shut down the project. Later, McKay was able to convince him to talk to Weir about allowing the two of them to return and restart the project. During the first test at half power, the device overloaded and McKay was unable to shut it down. The device then began releasing energy by discharging the weapon at the wreckage in orbit to prevent a catastrophic overload. Unable to prevent a full overload, they evacuated to the Puddle Jumper and had to avoid the weapons fire. Luckily, the Daedalus arrived and provided cover for their escape through the Stargate before the overload resulted in the destruction of 5/6th of the solar system. Back on Atlantis, McKay apologized but he told him it may take time for him to trust him again. (ATL: "Trinity")

Sheppard as a Bug-like creature.

On a mission to an unnamed planet, he learned that the villagers were being terrorized by what they call the Daimos. Their description of it is very similar to that of a Wraith. Ronon Dex offered his help in killing it but he ordered him to wait until morning and the whole team would go. The next day, Ronon successfully tracks a female Wraith into a cave. The team chases her inside but she hides behind a man named Zaddik. Zaddik explains that her name is Ellia and she does not feed because of a serum he created. He returned to Atlantis and explained the situation to Dr.Elizabeth Weir and Dr.Carson Beckett who volunteered to come to the planet to examine the serum and Ellia in the hope of perfecting his retrovirus. Once back in the cave, Teyla helped Ellia use her telepathic abilities to locate the adult Wraith that was killing the villagers. He, Teyla and Ronon left to kill it. When Ellia took Beckett's retrovirus and transformed into a creature closer to that of an Iratus bug, Teyla was knocked unconscious and Sheppard and Ronon were forced to kill her but not before she fed on Sheppard's arm. Back on Atlantis, Beckett noticed that Sheppard's wound had healed much faster than usual and that he was infected by the retrovirus. Sheppard later noticed that his former wound was slowly transforming him into a bug-like creature. Beckett attempted to slow it down by an inhibitor, but Sheppard was eventually transformed. Beckett came up with a plan to use Iratus bug embryonic stem cells to replace Sheppard's mutating cells. The team lead by MajorEvan Lorne first went to a planet with Iratus bugs but they were unable to get close enough to get any eggs without the bugs attacking. After Weir informed him of the situation, he escaped from his quarters. Several teams helped track him down and Ronon stunned him with his Particle magnum. The team was about to say goodbye to him, until Beckett realized that he had the pheromone to stop the bugs from attacking. He was able to get the eggs and was transformed back to Human again. (ATL: "Instinct", "Conversion")

He and his team traveled on the Daedalus to the Ancient ship Aurora. Since there was no life support they were forced to wear space suits when they beamed over. After Dr.Rodney McKay got life support functioning, he ordered Ronon Dex and Teyla Emmagan to search the ship and count the stasis pods. When McKay realized that the pods the crew was in was also a Virtual reality pod in addition to a stasis pod, he volunteered to enter one of the empty pods to contact the crew. After entering the virtual reality, he was arrested by one of the crew and taken to the Captain. He tried to explain that they are in stasis but the crew was unaware of their situation and placed him in the brig. He tried to convince First Officer Trebal to let him talk to the Captain again to convince him that Atlantis had been evacuated 10,000 years ago but she ignored his request. He then exited the pod and reentered in order to get the drop on the guard and escape. He cornered the Captain in his quarters and tried to explain but was shot by a Lantean stun weapon by Trebal and returned to the brig. After McKay entered the program and informed him that a Wraith was also in the program and two Wraith cruisers were on their way, he realized that the Wraith had to be First Officer Trebal. The two escaped from the brig and he went to the bridge to talk to the Captain again while McKay went to disconnect the Wraith. When he entered the bridge and told the Captain that Trebal was a Wraith, McKay was able to disconnect it and this proved the truth to the Captain. After the Captain gave him the self-destruct codes, he exited the pod just in time help McKay kill the Wraith. They set the self-destruct and beamed back to Daedalus before the Aurora blew and destroyed the cruisers. Back on Atlantis, he, his team, Dr.Elizabeth Weir and ColonelSteven Caldwell toasted the crew with Champagne. (ATL: "Aurora")

He and the team were taken by Lt.Aiden Ford's Coalition, to formulate a plan to destroy a WraithHive ship. Ronon Dex, Teyla Emmagan and Dr.Rodney McKay were dosed with the Wraith enzyme while he was kept clean in order to convince Dr.Elizabeth Weir that the enzyme was safe. After Ford explained the plan to use a Wraith Dart to plant C-4 on the Hive, he agreed to help but planned to use the Dart to dial Atlantis. After McKay fixed the Dart, Ford changed the plan and made McKay stay behind to ensure he kept his part of the bargain. He beamed everyone into the Dart and headed through the Stargate. While approaching the Hive the Dart went on Autopilot and forced Sheppard to unload his cargo blind. Most of Ford's men were beamed off a ledge. Believing Sheppard did it on purpose, Ford turned off his radio against Teyla's wishes. When Sheppard landed the alarms sounded and he was captured as were the others. Once in a cell the group managed to escape by using Ronon's knives to hit the door controls but they were quickly captured. The Wraith separated the team this time and put Sheppard in a cell with Ford and Neera, a girl they tried to rescue from a cocoon. While in the cell, Ford began to experience withdrawal and was taken by the Wraith Commander to a cocoon. After Neera attempted to get information from him, he realized she was a spy. He was then taken to see the Wraith Queen. While being questioned, he fooled the Queen into believing he was a Wraith worshipper for the Queen of the other Hive and was sent to kill her. Before the Queen could feed on him, Ford entered and shot her with Ronon's Particle magnum. While Ford drew the Wraith off, Sheppard freed Teyla and Ronon and beamed them into a Dart. After firing on the other Hive and forcing them to fight, Sheppard headed for the Spacegate and traveled to an uninhabited planet to release Ronon and Teyla. They then headed back to Atlantis. (ATL: "The Lost Boys", "The Hive")

On a mission to an unnamed planet, his team discovered a doorway. He attempted to cross the threshold and was pulled in. Ronon Dex and Teyla Emmagan tried to pull him out but were unsuccessful. After waking up on the other side in great pain, he waited in the cave for several hours trying to make radio contact but was unsuccessful. After several days, he began to run out of supplies and headed out of the cave. Once in the forest, he ran into Avrid who was being chased by a Beast. He fought the Beast but was badly injured and Avrid carried him back to the Cloister where his sister Hedda used her powers to heal his wounds. When he awoke, Teer and Avrid explained that the only way to escape was through ascension. After several months, Teer began to have feelings for him. When the Beast returned, he again attempted to defeat it but was badly injured. After several more months, Teer used her Telepathy to see that his team had come for him and that the Beast was upon them. He raced to their location and tried to fight the beast but the villagers came to help this time and defeated it with their powers before ascending. Dr.Rodney McKay then explained that he was trapped in a Time dilation field and was gone for only a few hours. (ATL: "Epiphany")

On a mission to the Lord Protector's Planet, he was scanned by Otho and taken to the Tower. Once inside, he noticed the resemblance to Atlantis and was introduced to the Lord Protector. He was invited to a feast where the Lord Protector became ill. Otho explained that it was not the first time and he called Dr.Carson Beckett to exam the Lord Protector. During the night, Mara came to him and ask for his hand in marriage. The next morning Otho explained that his Ancient Technology Activation gene was needed as the royal families gene was losing its potency. Beckett discovered that he was being poisoned little by little over the last several months. There was nothing he could do for him and he died a few hours later. Otho offered him their supply of Drone weapons and Puddle Jumpers in exchange for the Ancient Technology Activation gene therapy. After he delivered the therapy, Otho took it himself and had him and Beckett arrested. Later, Mara released him and told him Otho planned to kill the villagers with the Control chair. He ordered Dr.Rodney McKay to drain the Zero Point Module while he went to stop Otho and was able to stab Otho with his own poison knife. They gave the villagers a GDO in exchange for the Jumpers and Drones. (ATL: "The Tower")

After his team discovered two stasis pods in orbit in the Kohal system, they returned them to Atlantis. When Dr.Elizabeth Weir approached the pod, she was hit in the head with an energy beam and collapsed. When she awoke the consciousness of the pods inhabitant was transferred into her body. She explained that her name was Phoebus and the imprinting was temporary. Phoebus convinced Sheppard to allow the consciousness of her husband Thalan to enter him so she could say goodbye. After Thalan was transferred, Phoebus attacked Thalan and chased him through the city. Thalen's consciousness expired first (or pretended to), and Sheppard was able to stun Phoebus, before she would kill him. When he (or Thalen) asked Teyla Emmagan why she gave him the weapon, she responded that she knew that regardless of if it was Sheppard or Thalen they would have shot Weir with Sheppard knowing he was armed only with a stunner. He was taken to the infirmary and apologized for anything he might have said or done. (ATL: "The Long Goodbye")

When MajorEvan Lorne's team was attacked on M1K-177, he and his team went to assist but found the building badly burned. They discovered several bodies inside and one contained Lorne’s Dog tags. They returned the bodies to Atlantis and informed Dr.Elizabeth Weir. Moments later, Ladon Radim contacted Atlantis and Weir allowed him to come to Atlantis. He offered them a Zero Point Module for a supply of weapons so he could complete a coup d'etat against Cowen. Weir decided to inform Cowen instead in order to keep the loose alliance that was formed during the siege and he and Dr.Rodney McKay traveled to the Genii homeworld. Cowen was grateful for the heads up and they returned to Atlantis. He then came up with a plan to take the ZPM from Ladon and assembled a team to attack his building. Once inside they stunned several guards and came upon Ladon. Ladon handed over the ZPM but admitted that it was depleted and the doors closed and the room filled with gas. He awoke a short time later and Cowen revealed that it was his plan to lure him to the planet and use him to trade Weir for all their Puddle Jumpers. Cowen contacted Weir and gave her one hour to deliver the Jumpers or one of her people would be killed every 15 minutes starting with Sheppard. Ladon escorted him to a cell where Lorne and his men were being held. When the hour was up, Weir told Cowen that Ladon’s sister Dahlia Radim could be saved but he didn’t care and sent Ladon to kill Sheppard. When Ladon arrived he released them in exchange for his sister and they headed for the Stargate. After returning to Atlantis, Ladon detonated a Genii A-bomb on the planet and eliminated Cowen and his personal guard. Ladon returned to the Genii homeworld and assumed leadership of the Genii. (ATL: "Coup D'etat")

On a mission to Taranis, he had Dr.Rodney McKay work on the outposts malfunctioning shield while ChancellorLycus showed him the hanger which contained an Aurora-class battleship. When the planet began to suffer from tremors, McKay disvoered that the supervolcano that the outpost used as a power source was about to erupt. After Lycus was convinced to evacuate to Atlantis the Stargate fell into the lava. He had Teyla Emmagan and Ronon Dex escort people to the Daedalusbeam out locations and made McKay attempt to fix the Ancient ship which he named the Orion. When the conditions became worse and the Daedalus would not return in time, he evacuated all the remaining villagers to the Orion and McKay was able to fix the shields and hyperdrive and when the eruption occurred the ship was thrown clear of the hanger and the hyperdrive activated and transported the ship into orbit. When they returned to Atlantis, they discovered a Hive ship was on course for Atlantis. (ATL: "Inferno")

A few weeks later, Michael Kenmore brought a Hive ship to Atlantis and he was assigned by Dr.Elizabeth Weir to command the Orion. He waited outside of sensor range as Dr.Rodney McKay worked on restoring it's systems. When Michael explained that they ment them no harm and they wanted to use Dr.Carson Beckett's retrovirus to spread amongst their rival Wraith factions, he returned to Atlantis to discuss the proposal. After a meeting with his team, Weir and ColonelSteven Caldwell they agreed to an alliance. After a test of the retrovirus on a single Wraith, the Queen wanted to test it on an entire Hive. After the attempt failed and McKay came up with a plan to use the beaming technology on the Daedalus to test the retrovirus on the Hive, Weir assigned him to the Daedalus during the test. When the Daedalus exited hyperspace, they were attacked by both Hives. Caldwell attempted to beam a Nuclear warhead onto the Hive but the Jamming code prevented it. He then led a squadron of F-302 fighter-interceptors to take out the Hives hyperdrive. After destroying several Wraith Darts with the 302s Railguns and AIM 120A air-to-air missiles, two Darts were on his tail but were destroyed by MajorPat Meyers. Unable to get a shot at the hyperdrive, he latched onto the Hive before it entered hyperspace for Earth. While in hyperspace, he considered detaching but decided to wait until the ship left hyperspace. Once out of hyperspace, he attempted to contact McKay and Ronon Dex on the Hive but Michael was in possession of their radio and informed him that he was not aware of the plan to betray them and would soon be killed. Michael advised him to take out the hyperdrive. After hitting the first Hive with a missile, the Hives launched Darts and his 302 was damaged. He was brought on board and Michael tricked the Wraith into releasing him and they headed for McKay and Ronon. When the Daedalus and Orion arrived and attacked the Hives, he and Michael met up with McKay and Ronon who had escaped from their cocoons and boarded a Wraith scout ship. As soon as the scout ship left the Dart bay the Hive opened fire and he contacted the Daedalus to beam them over. Once on board the Daedalus, Caldwell targeted the Dart bay which took out the Hives weapons but the Daedalus took several hits and life support was knocked out. Unable to repair the system they beamed the retrovirus on the Hive and waited for it to take effect. After several hours and almost out of air, he led a team onto the Hive and rounded up the Human-form Wraith and put them into pods. When the entered the Queen's chamber she attacked MajorEvan Lorne, as females are immune to the retrovirus, and he and Ronon killed her. After beaming over the rest of the crew, Michael entered hyperspace for Atlantis with the Daedalus in tow. After returning to Atlantis, they removed the Wraith from stasis and Teyla Emmagan was able to pilot the Hive to M8G-352 and transferred the Wraith to the planet. After they left Beckett and a team there and returned to Atlantis, a Hive was detected heading towards M8G-352. Teyla again piloted the Hive to M8G-352 and rescued Beckett. He ordered the activation of the Nuclear warhead left as a failsafe by Michael and the others were able to override it. He then ordered McKay to fire on the camp. When the second Hive arrived, he and his team escaped on a Puddle Jumper and were rescued by the Daedalus. (ATL: "Allies", "No Man's Land", "Misbegotten")

When Lucius Luvin came to Atlantis and the rest of the expedition came under the influence of Lucius' herb, he remained ineffected due to the common cold he was suffering from. When he returned to Lucius' planet to investigate and his people were becoming ill, he tricked his wives into giving him a sample of the herb. When he returned Dr.Rodney McKay informed him that Dr.Carson Beckett, Teyla Emmagan and Ronon Dex went on a mission to M6H-491 to retrieve more herb for Lucius despite his order to shut down all gate activity. In order to cure Beckett, he kidnapped him and took him to the mainland in a Puddle Jumper to allow him to detox. When Beckett was cured, he allowed Ronon, Teyla and McKay to take him back to Atlantis and Beckett pretended to still be under the effect of the herb. When Beckett developed a cure and gave it to Lucius under the guise of giving him the Ancient Technology Activation gene therapy. When Lucius tried to fly a Jumper to test the gene, Beckett released him from the brig and boarded the Jumper. He flew the Jumper to the mainland to allow Beckett time to cure the rest of the expedition. (ATL: "Irresistible")

On a mission to an unnamed planet, he and his team were attacked by the villagers. They headed back to the Stargate but everyone but Dr.Rodney McKay were shot with tranquilizer darts. Fortunately, McKay was able to return to Atlantis after being shot in the glute by an arrow. He and the team woke up in a cage and Ronon Dex remembered having come to his planet as a Runner. Having stayed on this planet for too long caused the Wraith to attack it. The leader of the village, Keturah, was led to believe that the Wraith would no longer cull them in return for Ronon. Ronon grabbed a knife and threatened to kill himself if they didn't release his friends. Ketutah complied and released him and Teyla Emmagan. They returned to Atlantis and were greeted by MajorElliot Rutherford, who was preparing to mount a rescue mission. They grabbed weapons and headed back to the planet but it had already been culled. They returned to Atlantis and McKay was able to adjust the Long range sensors to find the location of the Wraith tracker on Ronon's homeworld Sateda. They traveled to Sateda on the Daedalus and found Ronon in an abandoned hospital. Ronon refused to leave without killing the Wraith Leader. He and Teyla, with the help of McKay and Dr.Carson Beckett, helped him fight off more of the Wraith hunting party, with Ronon leading the charge. Eventually, the entire Wraith hunting party composed of at least twenty-five individuals was wiped out. Ronon's wish was granted when the Wraith Leader came down to the planet's surface to fight Ronon one-on-one. Ronon was almost defeated until the timely intervention of Beckett and a Drone weapon. (Beckett had enough of seeing Ronon go through that and killed the Wraith saying "if he doesn't like it he can shoot me".) Beckett killed the Wraith, saving a grateful Ronon and they returned to Atlantis. (ATL: "Sateda")

When Dr.Rodney McKay found a reference to an Ancient experiment on the planet Asuras, his team and Dr.Elizabeth Weir traveled to the planet to make first contact with the Asurans. They were greeted by Niam and brought before the Asuran Council. After an unproductive meeting with the council, Weir met with their leader Oberoth in private about assisting in the fight the Wraith and trading for any Zero Point Modules they might by able to spare but he refused. Weir then decided to return to Atlantis but they were stopped and placed in the brig. They were then mind probed and the Asurans discovered that Atlantis was not destroyed as they believed. The Asurans took their City-ship into hyperspace and Niam informed them that they were on their way to Atlantis to destroy it. He explained that the Ancients created Nanites to fight the Wraith and the nanites replicated and assembled themselves into complex machines and eventually imitating the Ancients. When the Ancients lost control, they sent several warships to destroy them but several nanites survived and were able to replicate. Niam then offered to try to convince Oberoth to spare Atlantis if McKay would remove the aggressive nature from their Base code. McKay was able to reprogram Niam and freeze the rest of the Asurans. Weir decided that because Niam could not guarantee Atlantis' safety that they must destroy the City-ship. McKay was able to overload the ZPM's and they escaped on a Puddle Jumper before the city exploded. On the way back to Atlantis, Niam was reset by the other Asurans and attacked Weir. He and Ronon Dex forced him into the rear section and jettisoned him into space. (ATL: "Progeny")

After being asked to a planet for a meeting by the Genii, he and his team were attacked. They retreated to the Stargate but he was shot in the back with a harpoon and captured by CommanderAcastus Kolya. He was taken to another planet and imprisoned in a cell. He was then brought to a room and placed in front of a video camera that was communicating with Atlantis. Koyla demanded Ladon Radim be turned over to him in exchange for Sheppard's freedom, since it was Kolya who actually planned a coup against Cowen. After Dr.Elizabeth Weir refused, Kolya allowed a captured Wraith to feed a little off his life. He was returned to his cell and began to talk to the prisoner in the next cell who turned out to be the Wraith. He attempted to convince the Wraith to work with him to escape but the Wraith refused. After two more feedings, the Wraith finally agreed to help and the two jumped the guards arriving to take them to Kolya. They were able to fight their way to the surface and escape into the forest. Unsure of the direction of the Stargate, they waited in the forest for the rest of Sheppard's team to arrive. The next morning, Koyla's men discovered them and the Wraith fed on Sheppard to gain streangth. After killing the Genii, the Wraith returned all the years he took from him through the Gift of Life. Sheppard decided to drop him off on another planet and spared his life, but Kolya managed to escape again. (ATL: "Common Ground")

When MajorLeonard's team went missing on M1B-129, he and his team were sent in to search for them. After finding the bodies of several of the team as well as several Genii, they found a Wraithdevice. They headed back to the Stargate but Leonard used C-4 to blow up the Dial Home Device and then shot at them from the tree line. With the DHD destroyed they headed back to the Wraith device so Dr.Rodney McKay could shut it down. Once there the device began to effect everyone else but Teyla Emmagan because of her Wraith DNA. When Ronon Dex began to hallucinate, he and Teyla chased him through the forest and Teyla was shot in the leg by Leonard. Sheppard was able to find Leonard's camp and patch her wound but he to began to hallucinate. He had flashbacks to an unsanctioned mission to save the life of his friend, CaptainLyle Holland, whose Apache helicopter had crashed in Afghanistan. He came upon Leonard but was unable to stop him from committing suicide with a Fragmentation grenade. He shot at Ronon believing him to be a Taliban soldier. After returning to the cave and shooting McKay, Teyla was able to convince him to take her inside the cave and she deactivated the Wraith device. (ATL: "Phantoms")

He picked up Ronon Dex and Dr.Radek Zelenka after their camping trip to the mainland so Ronon could hunt for game while Zelenka preformed ground penetrating radar tests to test the dielectric permittivity of the region's subsurface. On the way back, the Puddle Jumpers navigation malfunctioned by Zelenka was able to fix it. When Dr.Rodney McKay discovered that the Flagisallus, presumably the same one who gave away McKay's position under the ocean, visited Atlantis. McKay took a look through the binoculars, and called him Sam, after Lt. ColonelSamantha Carter. When another Flagisallus arrived, he and McKay decided to take a Jumper for a closer look. When they got too close the echolocation began to effect them and he returned to Atlantis but not before their eardrums were damaged. However, at the same time people started to hallucinate several worried Ancient scientists. While recovering in the infirmary, McKay discovered a Bio lab in the database and investigated. They found that a device was being used by the Flagisallus to create the images in order to warn them of an impending Coronal mass ejection. He came up with a plan to use a Zero Point Module to strengthen the Daedalus'shield to deflect the ejection, which was successful. (ATL: "Echoes")

When the team encountered Lucius Lavin again, Ronon Dex took up Lucius' offer to hit him and almost broke his hand on his Personal shield emitter. Later, while trying to retake the village from CommanderAcastus Kolya, Ronon, Teyla Emmagan, Dr.Rodney McKay and Dr.Carson Beckett were captured but he was able to escape. After Lucius managed to slip away from Kolya's men and meet up with him, he took Lucius' shield and sent Lucius to round up the villagers. He entered the town and allowed the Genii to shoot him in the shield. With the Genii out of ammo, the villagers surrounded them and he ordered Kolya to surrender but Kolya went for his weapon and Sheppard was forced to kill him. (ATL: "Irresponsible")

After discovering a Society research lab in the first year of the expedition and believing it was a computer game, he and Dr.Rodney McKay began to compete against one another. A few years later, MajorEvan Lorne and his team visited M4D-058 and discovered that the game was real and a group of satellites was relaying information to Atlantis. He and his team traveled to the planet and was greated by Baden, the leader of Sheppard's country, named Hallona. He brought Baden to meet with Nola, the leader of McKay's country which he named Geldar, in order to negotiate a peace settlement. After having no success, they brought them both to Atlantis to explain that the differences between them was caused by their accidental interferece. While showing Baden the lab, Baden used it to order an attack on a Geldar mine. After returning to the planet, he and Teyla went with Baden to Hallona in order to prevent a full war. After the Daedalus arrived, McKay was able to simulate an endgame scenario to convince both sides that a real war would be devastating for both sides. (ATL: "The Game")

On the mandatory rest day, he attempted to teach Ronon Dex the sport of golf and Ronon taught him a Satedan hand to hand combat game. Later, they returned to Sheppard's quarters and drank beer and listened to music. After Dr.Carson Beckett was killed in an explosion, he was one of the pallbearers at his funeral. (ATL: "Sunday")

After Dr.Rodney McKay discovered a GeothermalMobile drilling platform, he and his team along with a group of scientists traveled by Puddle Jumper to the ocean floor. Once on station, Teyla Emmagan began to sense a Wraith presence. She reached out with her mind but found nothing. While McKay and the scientists worked in the control room he paired with Dr.Elizabeth Weir and Ronon Dex paired with Teyla to search the station. After Teyla attacked Ronon and knocked out the stations power, he and Weir came upon an unconscious Ronon. After hearing gunfire, they found Teyla disorientated with no memory of attacking Ronon or shutting down power throughout the station. She revealed that there was a Wraith Queen and it took control of her. He and Ronon went to search for her but were cut off by the forcefields. When Dr.Radek Zelenka disabled the field, he got to the Jumper and discovered Dr.Graydon's body. When he turned around the Queen used her Telepathy to force him to his knees. Before she could feed on him Ronon arrived and attempted to shot her. Unfortunately, Ronon missed and shot the front window of the Jumper causing the station to flood. Luckily, McKay was able to stop the water with the forcefield. The force of the water knocked the Queen out and they restrained her. After finding the Wraith cruiser and Teyla learning that the Queen set the self-destruct, he and McKay used the Ancient pressure suit to walk to the ship. After Teyla let the Queen escape and tricked her into believing he was going to fly the ship to safety, she swam back to the cruiset. After she disabled the self-destruct, he and McKay were able to kill her. (ATL: "Submersion")

Whilst he was on a routine resupply mission to an offworld base, his Puddle Jumper was disabled and was kidnapped by a race of people he would know as Travelers. They needed him to power a stranded Aurora-class battleship to help the race's population troubles. He sent the ship into hyperspace, but was later attacked by the Wraith. He worked with Larrin to deter the Wraith from the ship and was released when he proposed an alliance. (ATL: "Travelers")

He encountered Todd again, who proposed an alliance when the Asurans were wiping out Human worlds to stop the Wraith. They worked in trying to shutdown the Nanitebase code. After Dr.Rodney McKay and Jeannie Miller were kidnapped, he helped in breaking them out. However, nanites would attempt shut down Jeannie to heal her of her epilepsy. "Todd" was almost finished working on a way to shut down the nanites when he collapsed from hunger and needed a Human to feed on. Sheppard turned to Henry Wallace, the kidnapper, who had lost his daughter due to the nanites. He convinced Wallace to sacrifice his own life in order to shut down the nanites, as well as to prevent McKay from sacrificing his life. (ATL: "The Seer", "Miller's Crossing")

After his Organic Asuranclone brought the Core drive of an AsuranAurora-class battleship to him and his team, Sheppard aided in attempting to destroy the Asuran ships as they arrived to attack human worlds. During the first attack on the ships, Sheppard piloted the Apollo but seemed to return to Atlantis during the remaining attacks. When Dr.Rodney McKay came up with a plan to destroy the Asurans, Sheppard proposed an alliance with the Wraith to Todd as they needed a fleet for the plan. Sheppard and his team took Todd to visit his alliance and were stunned. After the negotiations were over, Todd revived Sheppard first and gave him back his gun before explaining that they had seven Hive ships willing to join them. Sheppard was unhappy as Todd promised at least a dozen but accepted that seven was better than nothing. On the way back to the Spacegate, what he believed to be an Asuran ship arrived, but it was really Larrin investigating the Wraith ships and Sheppard convinced her to talk to him. When he landed, he prevented her from killing Todd and ended up tied up by her during their conversation. Sheppard convinced Larrin to bring the Travelers into the growing fleet and was annoyed that she left him tied up when she went to try to convince the Traveler's governing council to help. After returning to Atlantis, he took Teyla Emmagan off active duty when he learned she was pregnant and was annoyed that McKay created FRAN. He then participated in the briefing with Larrin, Todd, ColonelSamantha Carter, ColonelAbraham Ellis and ColonelSteven Caldwell and was asked by Larrin, who brought six ships into the fleet, to be on her Aurora-class battleship during the Battle of Asuras as he was the best at firing its Drone weapons. Sheppard was unhappy but agreed. During the battle he destroyed a Aurora-class Asuran ship that tried to escape to hyperspace and suggested sending Nuclear warhead down to the planet after McKay was unable to overload the Zero Point Modules. When the ship returned to Atlantis, Sheppard asked for a way to contact Larrin in case he needed her help again for "professional reasons" and she promised to be in touch before the Apollobeamed him back to Atlantis. There he watched McKay remove Asuras from the database and headed off for lunch with him. (ATL: "This Mortal Coil", "Be All My Sins Remember'd")

A week after the Battle of Asuras, Sheppard decided to investigate Todd's tracking device being reactivated and found his Hive ship abandoned and his tracking device on the floor. Deciding to salvage the ship, Sheppard brought Teyla Emmagan in to fly it and explained his reasons for taking her off-duty which she didn't accept. On the ship, Dr.Rodney McKay informed him of the secret Wraith facility he wanted to check out and Sheppard refused at first, but finally agreed to take the Hive ship there after Teyla found she could easily fly it. After dropping out of hyperspace out of sensor range, Sheppard had Teyla stay behind to pilot the ship in order to protect her and as she was weakened from flying it there. On the planet, Sheppard witnessed the birth of Wraith warriors and rescued Todd (who he finally named) to get answers. Todd explained that it was a cloning facility and that it had been the key to their defeat of the Ancients as it gave them their numbers in the war. Sheppard, Ronon Dex and McKay were captured while Todd escaped to the Hive ship and the group was taken in front of the Wraith Queen who attempted to read his mind which he resisted and then attempted to feed on him, but was stopped by Teyla telepathically taking control of her after Todd alerted her to what was going on. Teyla, controlling the queen, rescued them and Sheppard killed the queen on her request, saving her and her baby. Unable to reach the Zero Point Modules, Sheppard had the team return to the Hive ship which he had Teyla crash into the facility, destroying it while he and eveyone but Todd (who escaped in a Wraith Dart) escaped in the Puddle Jumper and returned to Atlantis through the Spacegate after witnessing the facility destroyed. Later, Sheppard comforted Teyla who finally understood why he took her off the team and why she couldn't be on it while pregnant. (ATL: "Spoils of War")

He was one of the two pilots of Atlantis when it was returned to the Pegasus galaxy, and assisted in identifying the problem with the hyperdrive array on the east pier. This problem eventually caused Atlantis to drop out of hyperspace early, and meant Sheppard was forced to land the city on a new planet on the outskirts of the Pegasus galaxy. While on a mission to Manaria he released Todd (also known as Guide) back to his alliance to act as a counter to the rise of Queen Death to prominence among the Wraith. (ATL: "Legacy: Homecoming")

Sheppard is one of the most skilled fighters in Atlantis. He is able to use a wide a variety of Tau'ri and Wraith weapons. He was taught many Pegasus fighting styles by both Teyla Emmagan and Ronon Dex, although he regularly loses to the more experienced fighters. When the Genii temporarily seized control of the city he was able to drive them out almost single-handedly. He is also an outstanding snap-shooter, able to draw, fire, and hit his target with unaimed fire from the hip and one-handed. (ATL: "The Eye", "Irresponsible", "This Mortal Coil")

He is an exceptionally skilled pilot, being able to fly a wide variety of ships, ranging from Wraith Darts to AncientCity-ships. In fact, he has either piloted or assisted in piloting almost every known ship in the Pegasus Galaxy. He ranked first on the Chair Interface Aptitude list in Atlantis, which gave him a natural ability to pilot Ancient ships. He is a skilled fighter pilot, often flying an F-302 fighter-interceptor in space combat. His skill with Wraith Darts is less than with other vehicles, due to the unusual nature of Wraith technology and his lack of experience. Despite this, after having only piloted one once and assisted by a computer tablet translating that time, Sheppard was able to steal a Dart and fly it in the Battle of Edowin, ultimately leading to the destruction of two Hive ships as a result of his tactics and was later able to fly them with ease when needed. Before flying Atlantis the largest thing he had ever flown was a V-22 Osprey. Even though he had no experience in it, Sheppard quickly mastered flying a Travelergenerational ship, saying he had flown harder ships before. (ATL: "The Lost Boys", "The Hive", "No Man's Land", "First Strike", "The Lost Tribe", "Enemy at the Gate")

Despite having no psychic abilities beyond his Ancient Technology Activation gene, Sheppard has one of the most powerful mental defenses known. He is able to resist Hive Queens and Asuran mind-probes, albeit with difficulty. The only other person to display similar abilities was Lt. GeneralJack O'Neill who showed the ability to resist the Asuran mind-probe due to his previous encounters with it. When his team was temporarily placed in a mental illusions by the inhabitants of M5S-224, Sheppard displayed the ability to manipulate his own illusion, and was aware that something was wrong almost immediately. By 2008 he was able to completely resist a Queen, although it cost him a visible effort to do so. The Queen claimed he had the strongest resistance she had ever encountered from a human. Sheppard's ability to do this likely comes from the experience he gained fighting off multiple queens mind-probes. (ATL: "Home", "The Hive", "Progeny", "Spoils of War")

Sheppard is highly intelligent, as indicated by his passing of the Mensa entry test, which places him in the upper two percentile on standardized intelligence tests, although he never actually joined Mensa. However, he rarely shows off with this, thus surprising other people when he does. His high intelligence also gives him somewhat of an ability to keep up with Dr.Rodney McKay and his plans and also come up with his own brilliant tactical plans when he needs to. He is also a keen and talented golfer, although he is disappointed that no-one else on his team shares his enthusiasm. (ATL: "The Brotherhood", "Sunday")

Prior to coming to Atlantis, Sheppard's ability to form meaningful relationships with others was poor; he and his father hadn't spoken with each other for several years, and his marriage had fallen apart due to his inability to be there for her. However, since arriving in Atlantis, he has formed close bonds with several people, ranging from the senior staff to offworld allies.

Sheppard first met Larrin when she used a Traveler's ship to disable his Puddle Jumper and later captured him to use him to activate a Aurora-class battleship. At first they hated and distrusted each other. But after working together to rid the ship of Wraith and Sheppard saved Larrin's life from a Wraith that fed on her. She then thanked him and kissed him, but used it as an excuse to stun him. However, he was able to convince her to let him go, and she seemed impressed with him. Larrin later fought in the battle against the Asurans at his request, even requesting Sheppard be aboard her ship during the battle as she knew he was the best at using the ship's weapons. When it was over, Sheppard asked for a means of contacting her for "professional" reasons. He later ran into some Travelers and asked the Captain if Larrin ever mentioned him. She later mentioned she did after lying and saying she didn't. It's indicated that Larrin speaks very highly of him and his abilities. It is implied that should they meet again that their relationship might develop into something more. (ATL: "Travelers", "Be All My Sins Remember'd", "The Lost Tribe")

Easily the closest bonds Sheppard has formed since coming to Pegasus are the bonds he shares with his teammates on the First Atlantis Reconnaissance Team, although he and Dr.Meredith Rodney McKay are prone to the occasional argument, with McKay sometimes growing frustrated with Sheppard's apparent assumption that he can automatically save the day when scientific problems arise. The two have shown on many occasions that they have both a great esteem for the other's abilities and share a surprisingly close bond, with McKay commonly attempting to help Sheppard when he suffers from personal problems despite his own poor abilities with relationships, such as when he attempted to express his sympathies following the death of Sheppard's father. The two have also been shown to spend a surprising amount of their leisure time together, both of them playing what they initially believed to be a Civilization-like game before learning that it was an Ancient experiment with real people, and racing RC cars in the lower halls of Atlantis. The two also have a habit of risking their lives to save each other which McKay actually uses as an excuse to go after him once, saying it's his turn. Between their close bond, occasional bickering and deliberate attempts to annoy one another, and protective attitude toward each other, Sheppard's relationship with McKay can be seen as something of an attempt to recreate the bond he would have had with his younger brother, had the two of them not been estranged. Fans have even come to regard the relationship between McKay and Sheppard as a bromance of some sort with the pairing of the two being given the term, "McShep". (ATL: "Trinity", "Aurora", "The Game", "Outcast", "The Prodigal")

Although his bond with Lt.Aiden Ford never developed beyond simple friendship, Sheppard nevertheless clearly thought a great deal of the younger man, refusing to kill him even after he was driven half-insane by his use of the Wraith enzyme, and taking three years following their last encounter before he 'admitted' that Ford was almost certainly deceased. (ATL: "The Siege, Part 3", "The Hive", "Search and Rescue")

Sheppard is mostly estranged from his family. He had a wife, but they divorced after she couldn't take all of the secrets, although she did later come to understand how hard it must have been for him. His father and brother are successful businessmen and his father wanted him to be one too and they had a falling out when he wanted to join the United States Air Force. Sheppard felt he wasn't welcome by them afterwards and seemed to think he had no family as a result. He did return for his father's funeral and his brother thought he only wanted money from their father's will after being gone so long. His brother, Dave, revealed to him that his father always regretted their fight and wanted to make up but never got the chance, which seemed to stun Sheppard. After stopping a Replicator threat, Sheppard returned home to make up with his brother who seemed to accept him back into his life. (ATL: "Sateda", "Outcast")

Sheppard's relationship with the Wraith he named Todd is complicated. At first Sheppard hated Todd for feeding on him on CommanderAcastus Kolya's order, but formed an alliance with him to escape. Sheppard showed some trust in Todd, giving him a weapon and allowing him to lead the way. While the two agreed that "all bets are off" if they ever met again, they also agreed that in that case they never wanted to meet again so they wouldn't have to worry about that. The two kept their deal with each other and surprised each other at the same time: Todd returned Sheppard's life force that he took from him when Sheppard expected him to finish feeding on him and Sheppard returned Todd to the Wraith even though Todd expected him to kill him. Todd later used their familiarity to get to come to Atlantis during the Asuran threat, but Sheppard distrusted him then and whenever else they encountered him. Sheppard was willing to work with Todd when the situation called for it and believed him to be the best chance they had of defeating the Wraith, but always threatened to kill Todd if he needed to, though he admits that if Todd stopped being a Wraith he'd stop wanting to. Sheppard also keeps all the deals he makes with Todd who at least trusts him to do so as shown when Sheppard makes a deal for Todd to land a Hive ship in exchange for Sheppard allowing him to leave to seek a cure for a disease he was infected with. Sheppard also knows how to talk to Todd to get him to do things as shown when he convinces him to give up two Zero Point Modules for Atlantis causing Todd to comment "you know how to talk to me." (ATL: "Common Ground", "The Seer", "The Queen", "Infection", "Enemy at the Gate")

In another alternate reality, John was dishonorably discharged after attempting to rescue an unnamed medic, with whom he was romantically involved, in Afghanistan. This differs from our reality where he tried to save CaptainLyle Holland. His helicopter was shot down and the crash killed four American soldiers and eight civilians. After narrowly escaping jail time for political reasons, he moved to Las Vegas where he joined the Las Vegas Police Department. He was $13,000 in debt due to a gambling problem and only had about $2300 in his bank account. After four years of trying, he was finally promoted to Detective. Though this alternate version of John Sheppard was never married, he is still a fan of Johnny Cash, taking only a poster (the same one seen in his quarters on Atlantis in our reality) with him after resigning his position. While leaving town in 2009, he figured out where to find the Wraith that had been building a transmitter and tracked it down. He called Dr.Rodney McKay who sent two fighter jets to destroy the Wraith's transmitter, but not before John was shot in the chest. He is presumed dead because while trying to crawl away from the wreckage of the destroyed transmitter. He fell to the ground in the middle of the desert and was unable to move any farther. His fate was not revealed, though he appeared to be suffering severe blood loss. It is entirely possible that he perished shortly afterward. (ATL: "Vegas")

In another alternate reality visited by an alternate Rodney McKay in 2006, John Sheppard was likewise a member of the Atlantis expedition and the leader of AR-1. In 2009, that McKay told the Detective Sheppard of his reality that he had met his counterpart and that he was a hero who had saved the world several times over. Detective Sheppard commented that it did not sound much like him. However, McKay believed that there was little difference between the two Sheppards and that Detective Sheppard possessed the same strength of character. (ATL: "Vegas")

John Sheppard has the ability to instantly calculate certain difficult equations. For instance, in the season 1 episode "Home", he instantly knew it would take a Puddle Jumper 840 years to get to M5S-224 if Dr.Rodney McKay broke the Dial Home Device. However, it is possible that he calculated this up beforehand. In "Rising", he asked McKay to run through all the address combinations from the symbols Lt.Aiden Ford memorized, and when Dr.Rodney McKay asked Sheppard, "Do you have any idea how many combinations there are?" Sheppard instantly replied with "720." McKay seemed visibly taken aback by Sheppard's knowledge of that fact.